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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2024-11-20, 16:19 -05 based on data in: /media/carolinacastano/Datas 2/Sara/fastqc


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        General Statistics

        Showing 0/460 rows and 4/6 columns.
        Sample NameDupsGCAvg lenMedian lenFailedSeqs
        1-mRNA_1
        80.6%
        51.0%
        101bp
        101bp
        36%
        30.1M
        1-mRNA_2
        77.5%
        51.0%
        101bp
        101bp
        27%
        30.1M
        001T_1_R1
        49.8%
        51.0%
        150bp
        150bp
        10%
        69.9M
        001T_1_R2
        47.4%
        51.0%
        150bp
        150bp
        10%
        69.9M
        2-mRNA_1
        78.4%
        50.0%
        101bp
        101bp
        18%
        42.7M
        2-mRNA_2
        74.7%
        50.0%
        101bp
        101bp
        18%
        42.7M
        002T_1_R1
        53.8%
        42.0%
        150bp
        150bp
        10%
        94.9M
        002T_1_R2
        46.5%
        44.0%
        150bp
        150bp
        10%
        94.9M
        3-mRNA_1
        81.4%
        52.0%
        101bp
        101bp
        27%
        35.2M
        3-mRNA_2
        79.0%
        52.0%
        101bp
        101bp
        18%
        35.2M
        003T_1_R1
        60.4%
        41.0%
        150bp
        150bp
        20%
        97.9M
        003T_1_R2
        50.3%
        42.0%
        150bp
        150bp
        20%
        97.9M
        4-mRNA_1
        79.8%
        51.0%
        101bp
        101bp
        18%
        39.3M
        4-mRNA_2
        75.5%
        52.0%
        101bp
        101bp
        18%
        39.3M
        004T_1_R1
        59.4%
        41.0%
        150bp
        150bp
        20%
        81.6M
        004T_1_R2
        50.3%
        42.0%
        150bp
        150bp
        20%
        81.6M
        5-mRNA_1
        76.4%
        49.0%
        101bp
        101bp
        18%
        37.5M
        5-mRNA_2
        71.8%
        50.0%
        101bp
        101bp
        18%
        37.5M
        005T_1_R1
        49.7%
        49.0%
        150bp
        150bp
        10%
        69.3M
        005T_1_R2
        48.6%
        49.0%
        150bp
        150bp
        20%
        69.3M
        006T_1_R1
        61.2%
        42.0%
        150bp
        150bp
        20%
        113.3M
        006T_1_R2
        51.9%
        43.0%
        150bp
        150bp
        20%
        113.3M
        007T_1_R1
        61.6%
        41.0%
        150bp
        150bp
        20%
        114.7M
        007T_1_R2
        51.6%
        42.0%
        150bp
        150bp
        20%
        114.7M
        8-mRNA_1
        79.7%
        52.0%
        101bp
        101bp
        27%
        36.4M
        8-mRNA_2
        76.3%
        53.0%
        101bp
        101bp
        18%
        36.4M
        008T_1_R1
        46.3%
        46.0%
        150bp
        150bp
        20%
        77.0M
        008T_1_R2
        43.4%
        46.0%
        150bp
        150bp
        10%
        77.0M
        9-mRNA_1
        78.7%
        53.0%
        101bp
        101bp
        18%
        42.5M
        9-mRNA_2
        75.6%
        53.0%
        101bp
        101bp
        18%
        42.5M
        009T_1_R1
        62.3%
        42.0%
        150bp
        150bp
        20%
        94.2M
        009T_1_R2
        54.1%
        43.0%
        150bp
        150bp
        20%
        94.2M
        10-mRNA_1
        75.5%
        50.0%
        101bp
        101bp
        18%
        36.6M
        10-mRNA_2
        71.2%
        51.0%
        101bp
        101bp
        18%
        36.6M
        010T_1_R1
        61.5%
        40.0%
        150bp
        150bp
        20%
        99.3M
        010T_1_R2
        50.5%
        42.0%
        150bp
        150bp
        20%
        99.3M
        011T_1_R1
        43.7%
        46.0%
        150bp
        150bp
        20%
        74.7M
        011T_1_R2
        40.0%
        46.0%
        150bp
        150bp
        10%
        74.7M
        12-mRNA_1
        86.9%
        53.0%
        101bp
        101bp
        18%
        42.8M
        12-mRNA_2
        83.8%
        53.0%
        101bp
        101bp
        18%
        42.8M
        012T_1_R1
        47.0%
        50.0%
        150bp
        150bp
        10%
        74.0M
        012T_1_R2
        44.0%
        50.0%
        150bp
        150bp
        10%
        74.0M
        013T_1_R1
        61.2%
        41.0%
        150bp
        150bp
        20%
        124.0M
        013T_1_R2
        51.6%
        42.0%
        150bp
        150bp
        20%
        124.0M
        014T_1_R1
        58.7%
        43.0%
        150bp
        150bp
        20%
        98.6M
        014T_1_R2
        49.9%
        44.0%
        150bp
        150bp
        10%
        98.6M
        015T_1_R1
        38.5%
        45.0%
        150bp
        150bp
        20%
        69.9M
        015T_1_R2
        34.4%
        45.0%
        150bp
        150bp
        10%
        69.9M
        016T_1_R1
        45.3%
        48.0%
        150bp
        150bp
        20%
        65.4M
        016T_1_R2
        40.8%
        48.0%
        150bp
        150bp
        10%
        65.4M
        017T_1_R1
        54.8%
        41.0%
        150bp
        150bp
        20%
        88.4M
        017T_1_R2
        44.3%
        42.0%
        150bp
        150bp
        10%
        88.4M
        018T_1_R1
        58.1%
        41.0%
        150bp
        150bp
        20%
        79.7M
        018T_1_R2
        49.3%
        42.0%
        150bp
        150bp
        10%
        79.7M
        019T_1_R1
        63.8%
        43.0%
        150bp
        150bp
        20%
        96.6M
        019T_1_R2
        55.4%
        44.0%
        150bp
        150bp
        20%
        96.6M
        020T_1_R1
        56.9%
        41.0%
        150bp
        150bp
        20%
        95.9M
        020T_1_R2
        46.0%
        42.0%
        150bp
        150bp
        10%
        95.9M
        021T_1_R1
        70.0%
        41.0%
        150bp
        150bp
        20%
        109.8M
        021T_1_R2
        61.3%
        42.0%
        150bp
        150bp
        20%
        109.8M
        022T_1_R1
        41.7%
        46.0%
        150bp
        150bp
        10%
        71.6M
        022T_1_R2
        39.9%
        46.0%
        150bp
        150bp
        20%
        71.6M
        023T_1_R1
        56.1%
        41.0%
        150bp
        150bp
        10%
        98.0M
        023T_1_R2
        47.0%
        42.0%
        150bp
        150bp
        10%
        98.0M
        024T_1_R1
        45.6%
        46.0%
        150bp
        150bp
        20%
        72.4M
        024T_1_R2
        40.6%
        46.0%
        150bp
        150bp
        10%
        72.4M
        025T_1_R1
        51.4%
        42.0%
        150bp
        150bp
        20%
        73.2M
        025T_1_R2
        41.6%
        43.0%
        150bp
        150bp
        10%
        73.2M
        026T_1_R1
        58.9%
        41.0%
        150bp
        150bp
        20%
        88.2M
        026T_1_R2
        48.3%
        42.0%
        150bp
        150bp
        10%
        88.2M
        027T_1_R1
        45.1%
        45.0%
        150bp
        150bp
        20%
        70.9M
        027T_1_R2
        41.8%
        45.0%
        150bp
        150bp
        10%
        70.9M
        028T_1_R1
        63.5%
        41.0%
        150bp
        150bp
        20%
        118.5M
        028T_1_R2
        53.4%
        42.0%
        150bp
        150bp
        20%
        118.5M
        029T_1_R1
        61.8%
        41.0%
        150bp
        150bp
        20%
        97.9M
        029T_1_R2
        52.8%
        43.0%
        150bp
        150bp
        20%
        97.9M
        030T_1_R1
        48.1%
        47.0%
        150bp
        150bp
        10%
        70.6M
        030T_1_R2
        46.9%
        47.0%
        150bp
        150bp
        20%
        70.6M
        031T_1_R1
        45.3%
        46.0%
        150bp
        150bp
        10%
        67.3M
        031T_1_R2
        43.7%
        47.0%
        150bp
        150bp
        20%
        67.3M
        032T_1_R1
        66.7%
        42.0%
        150bp
        150bp
        20%
        91.0M
        032T_1_R2
        60.1%
        43.0%
        150bp
        150bp
        20%
        91.0M
        033T_1_R1
        40.7%
        45.0%
        150bp
        150bp
        20%
        69.6M
        033T_1_R2
        37.3%
        45.0%
        150bp
        150bp
        10%
        69.6M
        034T_1_R1
        58.9%
        41.0%
        150bp
        150bp
        20%
        77.9M
        034T_1_R2
        49.4%
        42.0%
        150bp
        150bp
        10%
        77.9M
        035T_1_R1
        58.9%
        41.0%
        150bp
        150bp
        20%
        82.1M
        035T_1_R2
        49.4%
        43.0%
        150bp
        150bp
        10%
        82.1M
        036T_1_R1
        63.9%
        42.0%
        150bp
        150bp
        20%
        97.5M
        036T_1_R2
        55.8%
        43.0%
        150bp
        150bp
        20%
        97.5M
        037T_1_R1
        44.9%
        48.0%
        150bp
        150bp
        10%
        69.2M
        037T_1_R2
        39.8%
        48.0%
        150bp
        150bp
        10%
        69.2M
        038T_1_R1
        54.0%
        42.0%
        150bp
        150bp
        10%
        90.8M
        038T_1_R2
        44.7%
        43.0%
        150bp
        150bp
        10%
        90.8M
        039T_1_R1
        57.4%
        41.0%
        150bp
        150bp
        20%
        96.0M
        039T_1_R2
        47.7%
        42.0%
        150bp
        150bp
        10%
        96.0M
        040T_1_R1
        55.9%
        41.0%
        150bp
        150bp
        20%
        80.9M
        040T_1_R2
        45.3%
        42.0%
        150bp
        150bp
        10%
        80.9M
        041T_1_R1
        59.4%
        41.0%
        150bp
        150bp
        20%
        104.2M
        041T_1_R2
        49.2%
        42.0%
        150bp
        150bp
        10%
        104.2M
        042T_1_R1
        44.3%
        48.0%
        150bp
        150bp
        10%
        69.3M
        042T_1_R2
        40.9%
        48.0%
        150bp
        150bp
        10%
        69.3M
        043T_1_R1
        60.4%
        41.0%
        150bp
        150bp
        20%
        115.5M
        043T_1_R2
        49.7%
        42.0%
        150bp
        150bp
        10%
        115.5M
        044T_1_R1
        57.7%
        40.0%
        150bp
        150bp
        20%
        84.2M
        044T_1_R2
        45.5%
        41.0%
        150bp
        150bp
        10%
        84.2M
        045T_1_R1
        46.3%
        48.0%
        150bp
        150bp
        10%
        70.1M
        045T_1_R2
        45.0%
        48.0%
        150bp
        150bp
        20%
        70.1M
        046T_1_R1
        45.0%
        46.0%
        150bp
        150bp
        20%
        70.1M
        046T_1_R2
        41.2%
        46.0%
        150bp
        150bp
        10%
        70.1M
        047T_1_R1
        56.6%
        41.0%
        150bp
        150bp
        20%
        90.1M
        047T_1_R2
        46.9%
        42.0%
        150bp
        150bp
        10%
        90.1M
        048T_1_R1
        59.8%
        42.0%
        150bp
        150bp
        20%
        96.2M
        048T_1_R2
        50.6%
        42.0%
        150bp
        150bp
        20%
        96.2M
        049T_1_R1
        43.8%
        47.0%
        150bp
        150bp
        20%
        72.7M
        049T_1_R2
        41.3%
        47.0%
        150bp
        150bp
        10%
        72.7M
        050T_1_R1
        57.5%
        41.0%
        150bp
        150bp
        20%
        85.4M
        050T_1_R2
        47.7%
        42.0%
        150bp
        150bp
        10%
        85.4M
        051T_1_R1
        40.3%
        47.0%
        150bp
        150bp
        10%
        66.6M
        051T_1_R2
        38.0%
        47.0%
        150bp
        150bp
        10%
        66.6M
        052T_1_R1
        41.0%
        50.0%
        150bp
        150bp
        10%
        70.1M
        052T_1_R2
        44.7%
        50.0%
        150bp
        150bp
        10%
        70.1M
        053T_1_R1
        45.6%
        49.0%
        150bp
        150bp
        10%
        66.9M
        053T_1_R2
        42.9%
        49.0%
        150bp
        150bp
        10%
        66.9M
        CME256003_R1
        48.8%
        50.0%
        101bp
        101bp
        27%
        64.5M
        CME256003_R2
        48.7%
        50.0%
        101bp
        101bp
        27%
        64.5M
        CME297594_R1
        42.3%
        49.0%
        101bp
        101bp
        27%
        34.2M
        CME297594_R2
        45.0%
        49.0%
        101bp
        101bp
        27%
        34.2M
        CT1_Clean_Data1
        58.9%
        47.0%
        140bp
        140bp
        27%
        22.9M
        CT1_Clean_Data2
        58.1%
        48.0%
        140bp
        140bp
        27%
        22.9M
        CT2_Clean_Data1
        69.1%
        48.0%
        140bp
        140bp
        27%
        19.2M
        CT2_Clean_Data2
        69.3%
        48.0%
        140bp
        140bp
        18%
        19.2M
        CT3_Clean_Data1
        64.8%
        48.0%
        140bp
        140bp
        27%
        22.6M
        CT3_Clean_Data2
        65.2%
        49.0%
        140bp
        140bp
        18%
        22.6M
        CT4_Clean_Data1
        67.6%
        48.0%
        140bp
        140bp
        27%
        21.3M
        CT4_Clean_Data2
        68.3%
        48.0%
        140bp
        140bp
        18%
        21.3M
        CT5_Clean_Data1
        63.3%
        49.0%
        140bp
        140bp
        27%
        22.0M
        CT5_Clean_Data2
        63.9%
        49.0%
        140bp
        140bp
        18%
        22.0M
        CT6_Clean_Data1
        63.0%
        48.0%
        140bp
        140bp
        27%
        21.0M
        CT6_Clean_Data2
        63.1%
        49.0%
        140bp
        140bp
        18%
        21.0M
        CT7_Clean_Data1
        55.7%
        48.0%
        140bp
        140bp
        27%
        21.5M
        CT7_Clean_Data2
        56.0%
        48.0%
        140bp
        140bp
        18%
        21.5M
        CT8_Clean_Data1
        56.7%
        48.0%
        140bp
        140bp
        27%
        19.9M
        CT8_Clean_Data2
        56.8%
        49.0%
        140bp
        140bp
        18%
        19.9M
        CT9_Clean_Data1
        69.1%
        47.0%
        140bp
        140bp
        27%
        22.0M
        CT9_Clean_Data2
        69.0%
        48.0%
        140bp
        140bp
        18%
        22.0M
        CT10_Clean_Data1
        59.3%
        47.0%
        140bp
        140bp
        27%
        22.5M
        CT10_Clean_Data2
        58.7%
        48.0%
        140bp
        140bp
        27%
        22.5M
        CT11_Clean_Data1
        69.0%
        47.0%
        140bp
        140bp
        27%
        20.5M
        CT11_Clean_Data2
        69.2%
        48.0%
        140bp
        140bp
        18%
        20.5M
        CT12_Clean_Data1
        59.9%
        48.0%
        140bp
        140bp
        27%
        22.5M
        CT12_Clean_Data2
        59.9%
        49.0%
        140bp
        140bp
        18%
        22.5M
        CT13_Clean_Data1
        67.1%
        47.0%
        140bp
        140bp
        27%
        21.6M
        CT13_Clean_Data2
        67.1%
        48.0%
        140bp
        140bp
        18%
        21.6M
        ERR2929716_1
        71.9%
        55.0%
        76bp
        76bp
        36%
        19.5M
        ERR2929716_2
        65.2%
        56.0%
        75bp
        76bp
        27%
        19.5M
        ERR2929717_1
        45.2%
        51.0%
        75bp
        76bp
        18%
        20.2M
        ERR2929717_2
        41.0%
        51.0%
        75bp
        76bp
        18%
        20.2M
        ERR2929718_1
        53.5%
        52.0%
        76bp
        76bp
        18%
        18.6M
        ERR2929718_2
        47.5%
        52.0%
        75bp
        76bp
        9%
        18.6M
        ERR2929719_1
        30.6%
        48.0%
        75bp
        76bp
        9%
        22.6M
        ERR2929719_2
        27.0%
        47.0%
        75bp
        76bp
        18%
        22.6M
        ERR2929720_1
        59.9%
        52.0%
        76bp
        76bp
        27%
        18.8M
        ERR2929720_2
        55.3%
        52.0%
        75bp
        76bp
        27%
        18.8M
        ERR2929721_1
        43.7%
        48.0%
        75bp
        76bp
        9%
        19.4M
        ERR2929721_2
        39.1%
        49.0%
        75bp
        76bp
        9%
        19.4M
        ERR2929722_1
        76.8%
        56.0%
        76bp
        76bp
        36%
        19.7M
        ERR2929722_2
        71.4%
        57.0%
        76bp
        76bp
        27%
        19.7M
        ERR2929723_1
        46.1%
        50.0%
        76bp
        76bp
        18%
        19.8M
        ERR2929723_2
        41.7%
        50.0%
        75bp
        76bp
        18%
        19.8M
        ERR2929724_1
        49.9%
        51.0%
        76bp
        76bp
        18%
        17.2M
        ERR2929724_2
        45.8%
        51.0%
        75bp
        76bp
        18%
        17.2M
        ERR2929725_1
        46.2%
        51.0%
        76bp
        76bp
        18%
        19.4M
        ERR2929725_2
        42.2%
        51.0%
        75bp
        76bp
        18%
        19.4M
        ERR2929726_1
        63.5%
        53.0%
        76bp
        76bp
        27%
        18.8M
        ERR2929726_2
        57.6%
        54.0%
        75bp
        76bp
        27%
        18.8M
        ERR2929727_1
        50.8%
        51.0%
        76bp
        76bp
        27%
        20.0M
        ERR2929727_2
        46.1%
        51.0%
        75bp
        76bp
        18%
        20.0M
        ERR2929728_1
        41.6%
        49.0%
        75bp
        76bp
        9%
        20.4M
        ERR2929728_2
        35.7%
        49.0%
        75bp
        76bp
        9%
        20.4M
        ERR2929729_1
        43.9%
        49.0%
        76bp
        76bp
        9%
        19.8M
        ERR2929729_2
        38.7%
        49.0%
        75bp
        76bp
        9%
        19.8M
        ERR2929730_1
        32.6%
        48.0%
        75bp
        76bp
        9%
        20.9M
        ERR2929730_2
        28.4%
        47.0%
        75bp
        76bp
        18%
        20.9M
        ERR2929731_1
        32.3%
        48.0%
        75bp
        76bp
        9%
        19.2M
        ERR2929731_2
        28.6%
        48.0%
        75bp
        76bp
        18%
        19.2M
        ERR2929732_1
        25.2%
        47.0%
        75bp
        76bp
        9%
        15.4M
        ERR2929732_2
        21.5%
        47.0%
        75bp
        76bp
        18%
        15.4M
        ERR2929733_1
        40.6%
        48.0%
        75bp
        76bp
        9%
        18.0M
        ERR2929733_2
        35.2%
        48.0%
        75bp
        76bp
        9%
        18.0M
        ERR2929734_1
        64.5%
        54.0%
        76bp
        76bp
        18%
        15.5M
        ERR2929734_2
        57.1%
        55.0%
        75bp
        76bp
        27%
        15.5M
        ERR2929735_1
        55.7%
        53.0%
        76bp
        76bp
        27%
        15.8M
        ERR2929735_2
        48.1%
        53.0%
        75bp
        76bp
        9%
        15.8M
        ERR2929736_1
        74.2%
        54.0%
        76bp
        76bp
        27%
        17.7M
        ERR2929736_2
        65.2%
        55.0%
        75bp
        76bp
        27%
        17.7M
        ERR2929737_1
        57.6%
        52.0%
        76bp
        76bp
        27%
        16.5M
        ERR2929737_2
        51.2%
        52.0%
        75bp
        76bp
        27%
        16.5M
        ERR2929738_1
        67.4%
        53.0%
        76bp
        76bp
        27%
        20.6M
        ERR2929738_2
        60.7%
        54.0%
        75bp
        76bp
        27%
        20.6M
        ERR2929739_1
        63.3%
        53.0%
        76bp
        76bp
        27%
        16.1M
        ERR2929739_2
        56.2%
        53.0%
        75bp
        76bp
        27%
        16.1M
        ERR2929740_1
        69.3%
        55.0%
        76bp
        76bp
        18%
        18.4M
        ERR2929740_2
        60.7%
        55.0%
        75bp
        76bp
        27%
        18.4M
        ERR2929741_1
        47.3%
        50.0%
        76bp
        76bp
        9%
        20.6M
        ERR2929741_2
        42.8%
        50.0%
        75bp
        76bp
        9%
        20.6M
        ERR2929743_1
        53.5%
        52.0%
        76bp
        76bp
        27%
        21.3M
        ERR2929743_2
        48.5%
        52.0%
        75bp
        76bp
        18%
        21.3M
        ERR2929744_1
        47.3%
        50.0%
        76bp
        76bp
        18%
        22.9M
        ERR2929744_2
        41.6%
        50.0%
        75bp
        76bp
        18%
        22.9M
        ERR2929745_1
        38.8%
        48.0%
        75bp
        76bp
        9%
        17.5M
        ERR2929745_2
        34.7%
        48.0%
        75bp
        76bp
        18%
        17.5M
        ERR2929746_1
        30.8%
        48.0%
        75bp
        76bp
        9%
        15.1M
        ERR2929746_2
        26.3%
        47.0%
        75bp
        76bp
        18%
        15.1M
        ERR2929747_1
        45.6%
        49.0%
        76bp
        76bp
        9%
        17.0M
        ERR2929747_2
        40.0%
        49.0%
        75bp
        76bp
        9%
        17.0M
        ERR2929748_1
        54.1%
        51.0%
        76bp
        76bp
        27%
        16.5M
        ERR2929748_2
        48.0%
        52.0%
        75bp
        76bp
        18%
        16.5M
        ERR2929749_1
        69.6%
        54.0%
        76bp
        76bp
        18%
        18.5M
        ERR2929749_2
        63.5%
        54.0%
        75bp
        76bp
        27%
        18.5M
        ERR2929750_1
        48.0%
        51.0%
        76bp
        76bp
        18%
        22.3M
        ERR2929750_2
        42.8%
        51.0%
        75bp
        76bp
        9%
        22.3M
        ERR2929751_1
        49.5%
        51.0%
        76bp
        76bp
        18%
        19.1M
        ERR2929751_2
        43.9%
        52.0%
        75bp
        76bp
        18%
        19.1M
        ERR2929752_1
        58.9%
        52.0%
        76bp
        76bp
        18%
        22.4M
        ERR2929752_2
        52.0%
        53.0%
        75bp
        76bp
        36%
        22.4M
        ERR2929753_1
        51.1%
        51.0%
        76bp
        76bp
        27%
        19.7M
        ERR2929753_2
        44.8%
        51.0%
        75bp
        76bp
        18%
        19.7M
        ERR2929754_1
        51.7%
        51.0%
        76bp
        76bp
        27%
        22.0M
        ERR2929754_2
        44.7%
        52.0%
        75bp
        76bp
        9%
        22.0M
        OVA1_1
        89.4%
        46.0%
        150bp
        150bp
        45%
        10.2M
        OVA1_2
        90.4%
        47.0%
        150bp
        150bp
        27%
        10.2M
        OVA2_1
        86.0%
        44.0%
        150bp
        150bp
        45%
        78.4M
        OVA2_2
        85.6%
        45.0%
        150bp
        150bp
        45%
        78.4M
        OVA3_1
        95.3%
        50.0%
        150bp
        150bp
        18%
        13.9M
        OVA3_2
        93.0%
        51.0%
        150bp
        150bp
        36%
        13.9M
        OVA4_1
        92.0%
        50.0%
        150bp
        150bp
        18%
        24.3M
        OVA4_2
        90.6%
        50.0%
        150bp
        150bp
        36%
        24.3M
        OVA5_1
        90.5%
        44.0%
        150bp
        150bp
        45%
        50.2M
        OVA5_2
        89.6%
        46.0%
        150bp
        150bp
        55%
        50.2M
        OVA6_1
        96.6%
        43.0%
        150bp
        150bp
        45%
        42.2M
        OVA6_2
        97.0%
        44.0%
        150bp
        150bp
        36%
        42.2M
        OVA7_1
        96.8%
        47.0%
        150bp
        150bp
        36%
        11.9M
        OVA7_2
        96.5%
        48.0%
        150bp
        150bp
        18%
        11.9M
        OVA8_1
        79.2%
        46.0%
        150bp
        150bp
        45%
        11.4M
        OVA8_2
        79.7%
        46.0%
        150bp
        150bp
        18%
        11.4M
        OVA9_1
        95.9%
        35.0%
        150bp
        150bp
        36%
        7.0M
        OVA9_2
        96.0%
        36.0%
        150bp
        150bp
        36%
        7.0M
        OVA10_1
        96.3%
        47.0%
        150bp
        150bp
        9%
        11.0M
        OVA10_2
        93.4%
        48.0%
        150bp
        150bp
        27%
        11.0M
        Q3.R1
        58.8%
        49.0%
        101bp
        101bp
        18%
        47.7M
        Q3.R2
        57.2%
        49.0%
        101bp
        101bp
        18%
        47.7M
        Q4.R1
        62.1%
        49.0%
        101bp
        101bp
        18%
        78.2M
        Q4.R2
        60.9%
        49.0%
        101bp
        101bp
        18%
        78.2M
        Q5.R1
        62.9%
        49.0%
        101bp
        101bp
        27%
        46.5M
        Q5.R2
        61.2%
        49.0%
        101bp
        101bp
        18%
        46.5M
        Q6.R1
        66.5%
        49.0%
        101bp
        101bp
        27%
        82.9M
        Q6.R2
        64.9%
        49.0%
        101bp
        101bp
        27%
        82.9M
        Q7.R1
        60.2%
        49.0%
        101bp
        101bp
        18%
        67.0M
        Q7.R2
        59.1%
        49.0%
        101bp
        101bp
        18%
        67.0M
        Q8.R1
        57.7%
        50.0%
        101bp
        101bp
        27%
        55.2M
        Q8.R2
        56.8%
        50.0%
        101bp
        101bp
        27%
        55.2M
        Q9.R1
        50.4%
        49.0%
        101bp
        101bp
        27%
        40.0M
        Q9.R2
        49.7%
        49.0%
        101bp
        101bp
        18%
        40.0M
        Q10.R1
        55.5%
        49.0%
        101bp
        101bp
        18%
        34.3M
        Q10.R2
        54.5%
        49.0%
        101bp
        101bp
        18%
        34.3M
        Q11.R1
        62.0%
        51.0%
        101bp
        101bp
        18%
        62.4M
        Q11.R2
        61.0%
        51.0%
        101bp
        101bp
        18%
        62.4M
        Q17.R1
        61.4%
        48.0%
        101bp
        101bp
        18%
        60.9M
        Q17.R2
        60.1%
        48.0%
        101bp
        101bp
        18%
        60.9M
        Q18.R1
        50.2%
        49.0%
        101bp
        101bp
        18%
        35.6M
        Q18.R2
        49.3%
        49.0%
        101bp
        101bp
        9%
        35.6M
        Q19.R1
        67.6%
        51.0%
        101bp
        101bp
        18%
        71.8M
        Q19.R2
        66.5%
        51.0%
        101bp
        101bp
        18%
        71.8M
        Q20.R1
        64.9%
        51.0%
        101bp
        101bp
        18%
        79.4M
        Q20.R2
        64.0%
        51.0%
        101bp
        101bp
        18%
        79.4M
        Q22.R1
        56.3%
        50.0%
        101bp
        101bp
        18%
        65.3M
        Q22.R2
        55.1%
        50.0%
        101bp
        101bp
        18%
        65.3M
        Q23.R1
        55.0%
        50.0%
        101bp
        101bp
        18%
        57.2M
        Q23.R2
        53.8%
        50.0%
        101bp
        101bp
        18%
        57.2M
        Q24.R1
        52.9%
        49.0%
        101bp
        101bp
        18%
        45.1M
        Q24.R2
        51.9%
        49.0%
        101bp
        101bp
        18%
        45.1M
        Q25.R1
        63.5%
        49.0%
        101bp
        101bp
        18%
        51.3M
        Q25.R2
        61.1%
        49.0%
        101bp
        101bp
        18%
        51.3M
        ST1_Clean_Data1
        67.2%
        48.0%
        140bp
        140bp
        27%
        21.8M
        ST1_Clean_Data2
        67.0%
        49.0%
        140bp
        140bp
        18%
        21.8M
        ST2_Clean_Data1
        69.0%
        48.0%
        140bp
        140bp
        27%
        23.3M
        ST2_Clean_Data2
        68.9%
        48.0%
        140bp
        140bp
        18%
        23.3M
        ST3_Clean_Data1
        66.2%
        48.0%
        140bp
        140bp
        27%
        22.2M
        ST3_Clean_Data2
        66.9%
        49.0%
        140bp
        140bp
        18%
        22.2M
        ST4_Clean_Data1
        77.5%
        47.0%
        140bp
        140bp
        27%
        23.4M
        ST4_Clean_Data2
        77.7%
        48.0%
        140bp
        140bp
        18%
        23.4M
        ST5_Clean_Data1
        67.8%
        48.0%
        140bp
        140bp
        27%
        22.5M
        ST5_Clean_Data2
        68.5%
        49.0%
        140bp
        140bp
        18%
        22.5M
        ST6_Clean_Data1
        68.7%
        48.0%
        140bp
        140bp
        27%
        23.7M
        ST6_Clean_Data2
        68.8%
        49.0%
        140bp
        140bp
        18%
        23.7M
        ST7_Clean_Data1
        63.5%
        48.0%
        140bp
        140bp
        27%
        23.3M
        ST7_Clean_Data2
        63.5%
        48.0%
        140bp
        140bp
        18%
        23.3M
        ST9_Clean_Data1
        69.8%
        50.0%
        140bp
        140bp
        27%
        20.1M
        ST9_Clean_Data2
        70.7%
        51.0%
        140bp
        140bp
        18%
        20.1M
        ST10_Clean_Data1
        69.4%
        48.0%
        140bp
        140bp
        27%
        22.4M
        ST10_Clean_Data2
        69.3%
        49.0%
        140bp
        140bp
        18%
        22.4M
        ST11_Clean_Data1
        60.6%
        48.0%
        140bp
        140bp
        27%
        19.2M
        ST11_Clean_Data2
        61.1%
        49.0%
        140bp
        140bp
        18%
        19.2M
        ST12_Clean_Data1
        73.4%
        48.0%
        140bp
        140bp
        27%
        21.5M
        ST12_Clean_Data2
        74.3%
        48.0%
        140bp
        140bp
        18%
        21.5M
        UTE1_1
        94.2%
        45.0%
        150bp
        150bp
        45%
        34.0M
        UTE1_2
        93.8%
        46.0%
        150bp
        150bp
        55%
        34.0M
        UTE2_1
        93.9%
        46.0%
        150bp
        150bp
        36%
        23.8M
        UTE2_2
        93.4%
        46.0%
        150bp
        150bp
        55%
        23.8M
        UTE3_1
        95.7%
        45.0%
        150bp
        150bp
        36%
        9.5M
        UTE3_2
        95.5%
        45.0%
        150bp
        150bp
        55%
        9.5M
        UTE4_1
        93.3%
        47.0%
        150bp
        150bp
        18%
        2.2M
        UTE4_2
        91.9%
        48.0%
        150bp
        150bp
        36%
        2.2M
        UTE5_1
        94.2%
        47.0%
        150bp
        150bp
        45%
        33.5M
        UTE5_2
        93.3%
        48.0%
        150bp
        150bp
        45%
        33.5M
        Z9926_309_1_1
        65.2%
        51.0%
        150bp
        150bp
        20%
        22.3M
        Z9926_309_1_2
        62.7%
        52.0%
        150bp
        150bp
        30%
        22.3M
        Z15417A1_1
        67.3%
        54.0%
        150bp
        150bp
        30%
        22.7M
        Z15417A1_2
        64.8%
        55.0%
        150bp
        150bp
        30%
        22.7M
        Z15761A1_1
        71.8%
        52.0%
        150bp
        150bp
        30%
        22.7M
        Z15761A1_2
        69.8%
        53.0%
        150bp
        150bp
        30%
        22.7M
        Z23723A1_1
        60.1%
        51.0%
        150bp
        150bp
        30%
        22.2M
        Z23723A1_2
        59.0%
        52.0%
        150bp
        150bp
        20%
        22.2M
        Z26119A1_1
        57.2%
        50.0%
        150bp
        150bp
        20%
        22.2M
        Z26119A1_2
        54.9%
        51.0%
        150bp
        150bp
        20%
        22.2M
        Z28034A1_1
        66.0%
        50.0%
        150bp
        150bp
        30%
        22.1M
        Z28034A1_2
        65.2%
        51.0%
        150bp
        150bp
        20%
        22.1M
        Z159419T_1
        60.1%
        52.0%
        150bp
        150bp
        30%
        22.5M
        Z159419T_2
        57.1%
        53.0%
        150bp
        150bp
        30%
        22.5M
        Z182046T_1
        56.5%
        52.0%
        150bp
        150bp
        30%
        22.0M
        Z182046T_2
        54.6%
        53.0%
        150bp
        150bp
        30%
        22.0M
        Z182806T_1
        60.8%
        50.0%
        150bp
        150bp
        20%
        22.1M
        Z182806T_2
        60.0%
        51.0%
        150bp
        150bp
        20%
        22.1M
        Z236740T_1
        64.1%
        50.0%
        150bp
        150bp
        30%
        22.6M
        Z236740T_2
        61.7%
        51.0%
        150bp
        150bp
        20%
        22.6M
        Z236978T_1
        76.9%
        47.0%
        150bp
        150bp
        30%
        23.1M
        Z236978T_2
        77.4%
        48.0%
        150bp
        150bp
        30%
        23.1M
        Z249013T_1
        69.8%
        56.0%
        150bp
        150bp
        30%
        19.3M
        Z249013T_2
        67.3%
        57.0%
        150bp
        150bp
        20%
        19.3M
        Z258030T_1
        62.2%
        51.0%
        150bp
        150bp
        20%
        22.4M
        Z258030T_2
        59.6%
        51.0%
        150bp
        150bp
        20%
        22.4M
        Z277554T_1
        67.3%
        49.0%
        150bp
        150bp
        30%
        22.0M
        Z277554T_2
        65.3%
        50.0%
        150bp
        150bp
        20%
        22.0M
        Z277914T_1
        64.8%
        49.0%
        150bp
        150bp
        30%
        22.6M
        Z277914T_2
        62.9%
        50.0%
        150bp
        150bp
        20%
        22.6M
        Z281495T_1
        60.1%
        53.0%
        150bp
        150bp
        30%
        24.0M
        Z281495T_2
        60.1%
        54.0%
        150bp
        150bp
        30%
        24.0M
        Z309396T_1
        65.5%
        53.0%
        150bp
        150bp
        30%
        22.5M
        Z309396T_2
        63.2%
        55.0%
        150bp
        150bp
        20%
        22.5M
        Z320719T_1
        67.5%
        51.0%
        150bp
        150bp
        20%
        22.2M
        Z320719T_2
        65.3%
        51.0%
        150bp
        150bp
        20%
        22.2M
        Z323330_130702T_1
        69.3%
        53.0%
        150bp
        150bp
        30%
        22.7M
        Z323330_130702T_2
        69.1%
        54.0%
        150bp
        150bp
        30%
        22.7M
        Z334618T_1
        67.5%
        57.0%
        150bp
        150bp
        20%
        22.7M
        Z334618T_2
        67.9%
        58.0%
        150bp
        150bp
        10%
        22.7M
        Z335722T_1
        65.7%
        52.0%
        150bp
        150bp
        20%
        22.0M
        Z335722T_2
        62.6%
        54.0%
        150bp
        150bp
        20%
        22.0M
        Z341526T_1
        61.7%
        51.0%
        150bp
        150bp
        20%
        22.3M
        Z341526T_2
        62.1%
        52.0%
        150bp
        150bp
        20%
        22.3M
        Z349088T_1
        69.3%
        58.0%
        150bp
        150bp
        20%
        22.8M
        Z349088T_2
        62.0%
        59.0%
        150bp
        150bp
        10%
        22.8M
        Z352108T_1
        57.0%
        49.0%
        150bp
        150bp
        20%
        23.2M
        Z352108T_2
        51.8%
        50.0%
        150bp
        150bp
        20%
        23.2M
        Z353517T_1
        65.6%
        52.0%
        150bp
        150bp
        30%
        23.3M
        Z353517T_2
        61.3%
        53.0%
        150bp
        150bp
        30%
        23.3M
        Z355528T_1
        59.6%
        52.0%
        150bp
        150bp
        30%
        23.1M
        Z355528T_2
        54.3%
        53.0%
        150bp
        150bp
        30%
        23.1M
        Z361834T_1
        57.0%
        50.0%
        150bp
        150bp
        30%
        24.0M
        Z361834T_2
        59.1%
        51.0%
        150bp
        150bp
        20%
        24.0M
        Z363835T_1
        66.0%
        57.0%
        150bp
        150bp
        20%
        23.5M
        Z363835T_2
        67.2%
        58.0%
        150bp
        150bp
        20%
        23.5M
        Z365019T_1
        58.0%
        51.0%
        150bp
        150bp
        20%
        22.0M
        Z365019T_2
        57.7%
        52.0%
        150bp
        150bp
        20%
        22.0M
        Z369691T_1
        51.1%
        50.0%
        150bp
        150bp
        20%
        23.1M
        Z369691T_2
        52.4%
        51.0%
        150bp
        150bp
        20%
        23.1M
        Z369742T_1
        61.0%
        52.0%
        150bp
        150bp
        20%
        24.0M
        Z369742T_2
        63.8%
        54.0%
        150bp
        150bp
        20%
        24.0M
        Z369939T_1
        58.5%
        51.0%
        150bp
        150bp
        30%
        23.1M
        Z369939T_2
        60.2%
        52.0%
        150bp
        150bp
        20%
        23.1M
        Z370989T_1
        64.0%
        50.0%
        150bp
        150bp
        30%
        21.9M
        Z370989T_2
        62.8%
        51.0%
        150bp
        150bp
        20%
        21.9M
        Z371587T_1
        61.2%
        53.0%
        150bp
        150bp
        30%
        23.3M
        Z371587T_2
        64.5%
        54.0%
        150bp
        150bp
        20%
        23.3M
        Z384610T_1
        61.1%
        52.0%
        150bp
        150bp
        20%
        22.5M
        Z384610T_2
        60.9%
        53.0%
        150bp
        150bp
        20%
        22.5M
        Z384960T_1
        60.8%
        57.0%
        150bp
        150bp
        20%
        19.6M
        Z384960T_2
        58.8%
        58.0%
        150bp
        150bp
        10%
        19.6M
        Z386901T_1
        62.3%
        50.0%
        150bp
        150bp
        20%
        22.7M
        Z386901T_2
        61.7%
        51.0%
        150bp
        150bp
        20%
        22.7M
        Z392626T_1
        60.0%
        51.0%
        150bp
        150bp
        30%
        22.6M
        Z392626T_2
        59.0%
        52.0%
        150bp
        150bp
        30%
        22.6M
        Z400282T_1
        65.1%
        50.0%
        150bp
        150bp
        30%
        22.5M
        Z400282T_2
        64.8%
        51.0%
        150bp
        150bp
        10%
        22.5M
        Z403294T_1
        57.3%
        50.0%
        150bp
        150bp
        20%
        22.6M
        Z403294T_2
        57.1%
        52.0%
        150bp
        150bp
        10%
        22.6M
        Z410250T_1
        71.4%
        55.0%
        150bp
        150bp
        20%
        22.7M
        Z410250T_2
        69.9%
        56.0%
        150bp
        150bp
        20%
        22.7M
        Z413736T_1
        66.6%
        53.0%
        150bp
        150bp
        30%
        22.6M
        Z413736T_2
        65.6%
        54.0%
        150bp
        150bp
        30%
        22.6M
        Z416681T_1
        55.3%
        52.0%
        150bp
        150bp
        30%
        22.0M
        Z416681T_2
        53.3%
        53.0%
        150bp
        150bp
        20%
        22.0M
        Z417036T_1
        60.1%
        50.0%
        150bp
        150bp
        20%
        22.4M
        Z417036T_2
        59.1%
        51.0%
        150bp
        150bp
        10%
        22.4M
        Z421280T_1
        54.8%
        51.0%
        150bp
        150bp
        20%
        22.1M
        Z421280T_2
        52.8%
        52.0%
        150bp
        150bp
        20%
        22.1M
        Z425623T_1
        59.1%
        52.0%
        150bp
        150bp
        20%
        22.0M
        Z425623T_2
        57.2%
        53.0%
        150bp
        150bp
        20%
        22.0M
        Z429938T_1
        61.0%
        51.0%
        150bp
        150bp
        30%
        22.7M
        Z429938T_2
        60.4%
        52.0%
        150bp
        150bp
        20%
        22.7M
        Z439345T_1
        67.0%
        50.0%
        150bp
        150bp
        30%
        20.6M
        Z439345T_2
        66.8%
        51.0%
        150bp
        150bp
        20%
        20.6M
        Z450984T_1
        59.8%
        52.0%
        150bp
        150bp
        30%
        22.1M
        Z450984T_2
        58.4%
        53.0%
        150bp
        150bp
        30%
        22.1M
        Z451015T_1
        52.5%
        50.0%
        150bp
        150bp
        20%
        22.1M
        Z451015T_2
        51.1%
        51.0%
        150bp
        150bp
        20%
        22.1M
        Z460874T_1
        65.2%
        53.0%
        150bp
        150bp
        30%
        22.0M
        Z460874T_2
        64.4%
        54.0%
        150bp
        150bp
        30%
        22.0M
        Z464893T_1
        63.9%
        50.0%
        150bp
        150bp
        30%
        22.6M
        Z464893T_2
        63.0%
        51.0%
        150bp
        150bp
        20%
        22.6M
        Z470249T_1
        60.9%
        50.0%
        150bp
        150bp
        20%
        22.5M
        Z470249T_2
        59.2%
        51.0%
        150bp
        150bp
        20%
        22.5M
        Z493611T_1
        59.9%
        51.0%
        150bp
        150bp
        30%
        22.1M
        Z493611T_2
        58.2%
        52.0%
        150bp
        150bp
        20%
        22.1M
        Z493925T_1
        70.0%
        58.0%
        150bp
        150bp
        20%
        22.3M
        Z493925T_2
        68.0%
        59.0%
        150bp
        150bp
        20%
        22.3M
        Z498825T_1
        65.5%
        50.0%
        150bp
        150bp
        20%
        22.6M
        Z498825T_2
        62.9%
        51.0%
        150bp
        150bp
        20%
        22.6M
        Z537822T_1
        68.4%
        51.0%
        150bp
        150bp
        20%
        22.5M
        Z537822T_2
        65.9%
        52.0%
        150bp
        150bp
        20%
        22.5M
        patient1-BulkGEX_Day0_R1
        73.6%
        42.0%
        151bp
        151bp
        18%
        60.8M
        patient1-BulkGEX_Day0_R2
        31.1%
        42.0%
        151bp
        151bp
        0%
        60.8M
        patient2-BulkGEX_Day0_R1
        76.5%
        43.0%
        151bp
        151bp
        18%
        62.0M
        patient2-BulkGEX_Day0_R2
        33.4%
        44.0%
        151bp
        151bp
        0%
        62.0M
        patient3-BulkGEX_Day0_R1
        77.6%
        47.0%
        151bp
        151bp
        27%
        88.7M
        patient3-BulkGEX_Day0_R2
        66.9%
        49.0%
        151bp
        151bp
        18%
        88.7M
        patient4-BulkGEX_Day0_R1
        69.9%
        48.0%
        151bp
        151bp
        27%
        111.9M
        patient4-BulkGEX_Day0_R2
        61.9%
        49.0%
        151bp
        151bp
        27%
        111.9M
        patient5-BulkGEX_Day0_R1
        64.5%
        48.0%
        151bp
        151bp
        36%
        85.8M
        patient5-BulkGEX_Day0_R2
        56.2%
        49.0%
        151bp
        151bp
        36%
        85.8M
        patient6-BulkGEX_Day0_R1
        78.1%
        47.0%
        151bp
        151bp
        18%
        87.4M
        patient6-BulkGEX_Day0_R2
        67.3%
        48.0%
        151bp
        151bp
        9%
        87.4M
        patient7-BulkGEX_Day0_R1
        60.1%
        41.0%
        151bp
        151bp
        18%
        73.5M
        patient7-BulkGEX_Day0_R2
        51.6%
        42.0%
        151bp
        151bp
        9%
        73.5M
        patient8-BulkGEX_Day0_R1
        52.7%
        45.0%
        151bp
        151bp
        27%
        75.7M
        patient8-BulkGEX_Day0_R2
        43.6%
        45.0%
        151bp
        151bp
        0%
        75.7M
        patient9-BulkGEX_Day0_R1
        69.5%
        46.0%
        151bp
        151bp
        36%
        61.3M
        patient9-BulkGEX_Day0_R2
        59.4%
        47.0%
        151bp
        151bp
        27%
        61.3M
        patient10-BulkGEX_Day01_R1
        53.4%
        44.0%
        151bp
        151bp
        27%
        61.0M
        patient10-BulkGEX_Day01_R2
        42.6%
        44.0%
        151bp
        151bp
        9%
        61.0M
        patient10-BulkGEX_Day02_R1
        57.0%
        43.0%
        151bp
        151bp
        18%
        61.6M
        patient10-BulkGEX_Day02_R2
        46.1%
        44.0%
        151bp
        151bp
        9%
        61.6M
        patient11-BulkGEX_Day0_R1
        51.3%
        45.0%
        151bp
        151bp
        36%
        88.6M
        patient11-BulkGEX_Day0_R2
        41.6%
        45.0%
        151bp
        151bp
        18%
        88.6M
        patient12-BulkGEX_Day0_R1
        51.2%
        46.0%
        151bp
        151bp
        45%
        84.2M
        patient12-BulkGEX_Day0_R2
        43.3%
        46.0%
        151bp
        151bp
        36%
        84.2M
        patient13-BulkGEX_Day01_R1
        49.2%
        44.0%
        151bp
        151bp
        27%
        64.8M
        patient13-BulkGEX_Day01_R2
        40.2%
        45.0%
        151bp
        151bp
        18%
        64.8M
        patient13-BulkGEX_Day02_R1
        53.0%
        45.0%
        151bp
        151bp
        45%
        93.5M
        patient13-BulkGEX_Day02_R2
        43.9%
        45.0%
        151bp
        151bp
        18%
        93.5M

        FastQC

        Version: 0.11.9

        Quality control tool for high throughput sequencing data.URL: http://www.bioinformatics.babraham.ac.uk/projects/fastqc

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Created with MultiQC

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Created with MultiQC

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Created with MultiQC

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Created with MultiQC

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Created with MultiQC

        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Created with MultiQC

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (e.g. PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Created with MultiQC

        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Created with MultiQC

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 0/20 rows and 3/3 columns.
        Overrepresented sequenceReportsOccurrences% of all reads
        CTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTCCTACAAATGGACCTT
        60
        24813408
        0.1240%
        GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        50
        2764556
        0.0138%
        GGGCGATCTGGCTGCGACATCTGTCACCCCATTGATCGCCAGGGTTGATT
        47
        6392810
        0.0319%
        CTGGCTGCGACATCTGTCACCCCATTGATCGCCAGGGTTGATTCGGCTGA
        46
        9195575
        0.0460%
        CCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATG
        46
        5358852
        0.0268%
        GTCTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTCCTACAAATGGACC
        43
        5581802
        0.0279%
        CTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGGT
        42
        3622433
        0.0181%
        CCCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATAT
        42
        3597302
        0.0180%
        CCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATT
        42
        3240017
        0.0162%
        GTAAAACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAAT
        42
        2267229
        0.0113%
        CCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCA
        36
        3692123
        0.0185%
        CTCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATC
        36
        4837255
        0.0242%
        GTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAGTTCGG
        34
        1886622
        0.0094%
        GTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGA
        33
        2597336
        0.0130%
        TTTTTATTTATTTTTATTTTATTTTATTTTTTATTTTTTTTTTTTTTTTT
        32
        14564233
        0.0728%
        ATTTTTTATTTATTTTTATTTTATTTTATTTTTTATTTTTTTTTTTTTTT
        32
        7027934
        0.0351%
        GCCCTCTTGAACTCTCTCTTCAAAGTTCTTTTCAACTTTCCCTTACGGTA
        32
        1898780
        0.0095%
        CTCAGACCGCGTTCTCTCCCTCTCACTCCCCAATACGGAGAGAAGAACGATCATCAATGGCTGACGGCAGTTGC
        32
        1863364
        0.0093%
        GGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGA
        32
        4029660
        0.0201%
        CTTGGAAGCTTGACTACCCTACGTTCTCCTACAAATGGACCTTGAGAGCT
        31
        6195932
        0.0310%

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Created with MultiQC

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        FastQC0.11.9